Eutrophication has become one of the most serious problems threatening the lakes/reservoirs in China over 50 years. Evaluation of eutrophication is a multi-criteria decision-making process with uncertainties. In this study, a cloud matter element (CME) model was developed in order to evaluate eutrophication level objectively and scientifically, which incorporated the randomness and fuzziness of eutrophication evaluation process. The elements belonging to each eutrophication level in the CME model were determined by means of certainty degrees through repeated simulations of cloud model with reasonable parameters of expectation , entropy , and hyper-entropy . The weights of evaluation indicators were decided by a combination of entropy technology and analytic hierarchy process method. The neartudes of water samples to each eutrophication level of lakes/reservoirs in the CME model were generated and the eutrophication levels were determined by maximum neartude principal. The proposed CME model was applied to evaluate eutrophication levels of 24 typical lakes/reservoirs in China. The results of the CME model were compared with those of comprehensive index method, matter element model, fuzzy matter element model, and cloud model. Most of the results obtained by the CME model were consistent with the results obtained by other methods, which proved the CME model is an effective tool to evaluate eutrophication.